Sources including SCIENCE magazine have parsed the funding in the new continuing resolution covering FY17, and it's not terrible - in most ways.
The big cuts feared by science advocates are not in this bill. NASA does more than ok with $19.653 billion for the whole fiscal year. Indeed, NASA does a lot better overall than was projected by the last Obama budget, with the biggest increase coming in the Exploration account, which includes human exploration, a favorite of the new President. Planetary science went up, and Earth science, a likely future target, gets the same amount as in FY16.
Basic and applied research goes up, and both military and civilian agencies benefit. The EPA's research budget took a major hit, though, and the Department of Energy's fusion-power research was hammered, which has international implications given the consortium on the ITER experiment would have to push out their deadlines (at best) without U.S funding. (Also, my personal opinion is that anything that moves us closer to fusion power needs a MAJOR increase, not a cut.) The Congress controlled by the President's party poked him in the eye, sharply, with a $2 billion increase for NIH.
President Trump's FY18 budget is another matter: it's the one that slashes much more funding for the EPA and biomedical research, among other things.
So the major battles lie ahead...